GaAs/Al-GaAs core-shell nanowires fabricated by molecular beam epitaxy contain quantum confining structures susceptible of producing narrow photoluminescence (PL) and single photons. The nanoscale chemical mapping of these structures is analyzed in 3D by atom probe tomography (APT). The study allows us to confirm that Al atoms tend to segregate within the AlGaAs shells towards the vertices of the hexagons defining the nanowire cross section. We also find strong alloy fluctuations remaining AlGaAs shell, leading occasionally to the formation of quantum dots (QDs). The PL emission energies predicted in the framework of a 3D effective mass model for a QD analyzed by APT and the PL spectra measured on other nanowires from the same growth batch are consistent within the experimental uncertainties. (C) 2014 AIP Publishing LLC.